Estimates of fish biomass collated at the community level are reliable indicators of fish and ecosystem health. Data to calculate fish biomass is routinely collected using either underwater visual census (UVC) or stereo diver operated video (DOV), although the compatibility of UVC and DOV based estimates are yet to be assessed. Accordingly, we calculated and compared community level measures of coral reef fish biomass at Ningaloo reef (Western Australia) using both UVC and DOV. The UVC based biomass estimates were 788 kg/Ha, which was ∼50% greater than those from DOV (500 kg/Ha). Differences between the methods were primarily due to DOV measuring the length of only ∼40% of fish detected by video, preventing fish specific weight calculations for all fish encountered. When the size of unmeasured fish was assumed to be the median value of fish measured by DOV, revised DOV+ estimates of community biomass (778 kg/Ha) were similar to those from UVC. However, even when unmeasured fish were included in DOV calculations, biomass of some families (serranids) were still higher when using UVC. Conversely, DOV adjusted estimates of pomacentrid biomass were higher than those from UVC, due to DOV measuring fewer small bodied fish (<3 cm), thus having a larger median size for the high number of unmeasured pomacentrids compared to UVC. Our results suggest that community measures of fish biomass from DOV and UVC are broadly comparable once weights of unmeasured fish are incorporated into DOV estimates. This may increase the spatial and temporal scales at which fish biomass can be monitored, although compatibility of data will depend on the composition and size distribution of the fish assemblages.